
import os

PWD = os.path.dirname(__file__)
REF_DIR = "/Users/mjquist/Desktop/bio-references/"

KNOWN_GENE_TABLE = REF_DIR + "mergedGeneCluster-plus-additional.table.txt"

GENOME_DIR = REF_DIR + "hg19"

CODON_TABLE = PWD + "snps/codon-table-2.txt"
BLOSUM_MATRIX = PWD + "snps/blosum62.txt"

SHENDURE_SNP_FILE = REF_DIR + "known_snps/shendure_snps.txt"
DBSNP_FILE = REF_DIR + "known_snps/snp131-singles.sorted-dbsnp.INDEX"
PHASTCONS_INFO_PATH = REF_DIR + "phastcons"

CODON_INFO_PATH = REF_DIR + "ucsc_codon_info"
UCSC_KNOWN_GENE_TABLE = PWD + "/snps/knownGene.table.txt"
UCSC_KG_XREF_TABLE = PWD + "/snps/kgXref.table.txt"

CCDS_CODON_INFO_PATH = REF_DIR + "ccds_codon_info"
CCDS_KNOWN_GENE_TABLE = REF_DIR + "ccds_codon_info/ccdsGene.table.txt"
CCDS_GENE_NAMES = REF_DIR + "ccds_codon_info/ccdsToGene.via-SureSelect.txt"

